Basingstoke Bison left the league and joined the British National League. The London Knights were formed and joined the ISL playing out of London Arena. The Newcastle franchise also changed their name from the Newcastle Cobras to the Newcastle Riverkings.
Losing the Daily Express sponsorship, the Express Cup was renamed the Challenge Cup. The competition was also integrated into the league fixtures with the first round of games between teams (home and away) counting towards the Challenge Cup table and the league table. The league season was therefore increased to forty-two rounds.
The Benson & Hedges Cup consisted of the teams from the ISL and the top teams from the British National League. In the 1998–99 season, sixteen teams in total were split into four groups (two ISL and two BNL) playing each team in their group once at home and once away. All sixteen teams then progressed to a challenge round of a home and away game with the winners on aggregate progressing. The quarter finals and semi finals were also home and away aggregate rounds with the final being a one off game held at Sheffield Arena.
Note: The first home team is shown first
All eight teams in the league competed in the newly renamed Challenge Cup. The first round was the first home and away meeting of each team in the league with the points counting towards both the Challenge Cup table and the league table. The top four teams progressed to the semi finals. The semi finals were home and away games with the winner on aggregate progressing to the one off final game.